A few days ago, several users have reported that their saves in Pokemon X and Y have been getting corrupted, resulting in the game booting up strangely. Whether it was widespread, is still unknown, mostly because everyone after that was careful enough not to save anywhere near Lumiose.
Thankfully Nintendo has heard the cries of those affected and is apparently working on a fix. In the image posted, you can see the area highlighted in blue, where you should not be saving your game. Everywhere else is OK. Although, buildings in those blue areas are completely fine.
According to this very broken translation thanks to Google Translate, Nintendo is working on a fix and will push it soon:
We are gearing up where I am allowed to deliver from "Nintendo e-shop" in a few days to repair your reports the "fix". As soon as it is ready, so I will inform you again, I ask to have you wait for a while now.
Essentially, they're saying hold tight, don't save in the blue area, and they'll have a fix before you know it.
